On Aug 31, 2011, at 4:00 PM, Yuri Pompeu wrote:
After i get my output file from baverage containing the average b-
factor and rms by residues,
How can I calculate and display the average (and or mean) B-factors?
Is there a way of calculating it by protein, ligands and solvent
separately?
Chimera's Render by Attribute tool can depict atoms by their B-factor
or residues by their average B-factor (assuming you have a PDB file
with a B-factor column). It also shows a histogram of the B-factor
values. You can use the Attribute Calculator tool to compute the
average B-factor of any part of your structure and write it to a file.
Some links:
Chimera: www.cgl.ucsf.edu/chimera
Render by Attribute:
www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/render/render.html
Attribute Calculator:
www.cgl.ucsf.edu/chimera/current/docs/ContributedSoftware/calculator/calculator.html
a tutorial focused on coloring by B-factor:
www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/bfactor.html
--Eric
Eric Pettersen
UCSF Computer Graphics Lab
http://www.cgl.ucsf.edu
